got rid of last uses of six

mhctools/__init__.py

@@ -47,6 +47,8 @@
     "NetMHCpan41",
     "NetMHCpan4_BA",
     "NetMHCpan4_EL",
+    "NetMHCpan41_BA", 
+    "NetMHCpan41_EL",
     "NetMHCIIpan",
     "NetMHCIIpan3",
     "NetMHCIIpan4",

mhctools/base_commandline_predictor.py

@@ -18,7 +18,6 @@
 from subprocess import check_output
 import tempfile
 
-from six import string_types
 from typechecks import require_string, require_integer, require_iterable_of
 from mhcnames import normalize_allele_name, AlleleParseError
 
@@ -128,14 +127,14 @@ def __init__(
         require_string(allele_flag, "Allele flag")
         self.allele_flag = allele_flag
 
-        require_iterable_of(peptide_mode_flags, string_types)
+        require_iterable_of(peptide_mode_flags, str)
         self.peptide_mode_flags = peptide_mode_flags
 
         if tempdir_flag is not None:
             require_string(tempdir_flag, "Temporary directory flag")
         self.tempdir_flag = tempdir_flag
 
-        require_iterable_of(extra_flags, string_types)
+        require_iterable_of(extra_flags, str)
         self.extra_flags = extra_flags
 
         require_integer(

mhctools/base_predictor.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2014-2017. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,11 +10,9 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
 import logging
 from collections import defaultdict
 
-from six import string_types
 from typechecks import require_iterable_of
 from mhcnames import normalize_allele_name
 
@@ -68,11 +64,11 @@ def __init__(
         """
         # I find myself often constructing a predictor with just one allele
         # so as a convenience, allow user to not wrap that allele as a list
-        if isinstance(alleles, string_types):
+        if type(alleles) is str:
             alleles = alleles.split(',')
         self.alleles = self._check_hla_alleles(alleles, valid_alleles)
 
-        if isinstance(default_peptide_lengths, int):
+        if type(default_peptide_lengths) is int:
             default_peptide_lengths = [default_peptide_lengths]
         require_iterable_of(default_peptide_lengths, int)
         self.default_peptide_lengths = default_peptide_lengths
@@ -156,7 +152,7 @@ def _check_peptide_inputs(self, peptides):
         """
         Check peptide sequences to make sure they are valid for this predictor.
         """
-        require_iterable_of(peptides, string_types)
+        require_iterable_of(peptides, str)
         check_X = not self.allow_X_in_peptides
         check_lower = not self.allow_lowercase_in_peptides
         check_min_length = self.min_peptide_length is not None
@@ -188,7 +184,7 @@ def predict_subsequences(
         and an optional list of peptide lengths, returns a
         BindingPredictionCollection.
         """
-        if isinstance(sequence_dict, string_types):
+        if isinstance(sequence_dict, str):
             sequence_dict = {"seq": sequence_dict}
         elif isinstance(sequence_dict, (list, tuple)):
             sequence_dict = {seq: seq for seq in sequence_dict}

mhctools/binding_prediction.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2014-2019. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 import numpy as np
 from serializable import Serializable
 
@@ -40,7 +36,7 @@ def __init__(
         score : float
             Continuous prediction of peptide-MHC binding where larger values
             indicate either higher affinity or higher probability. For affinity
-            predictors this can be 1-log(IC50)/log(max_IC50) For mass spec
+            predictors this can be 1-log(IC50)/log(max_IC50). For mass spec
             predictors this can be the probability of detection.
 
         percentile_rank : float

mhctools/cleanup_context.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2014-2017. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,7 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
 import logging
 import os
 import shutil

mhctools/common.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2014-2019. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,17 +10,13 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
-from six import string_types
-
 def seq_to_str(obj, sep=","):
     """
     Given a sequence convert it to a comma separated string.
     If, however, the argument is a single object, return its string
     representation.
     """
-    if isinstance(obj, string_types):
+    if type(obj) is str:
         return obj
     elif isinstance(obj, (list, tuple)):
         return sep.join([str(x) for x in obj])

mhctools/iedb.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2014-2019. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,15 +10,13 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
 import io
 
 # pylint: disable=import-error
-from six.moves.urllib.request import urlopen, Request
+from urllib.request import urlopen, Request
 # pylint: disable=import-error
-from six.moves.urllib.parse import urlencode
+from urllib.parse import urlencode
 
-from six import string_types
 
 import pandas as pd
 import numpy as np

mhctools/input_file_formats.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2014-2017. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,7 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
 import tempfile
 
 def make_writable_tempfile(prefix_number, prefix_name, suffix):

mhctools/logging.py

@@ -1,4 +1,14 @@
-from __future__ import print_function, division, absolute_import
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
 
 import logging
 import logging.config

mhctools/mhcflurry.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2017. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,7 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
 import logging
 
 from numpy import nan

mhctools/mixmhcpred.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2019. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 import pandas as pd
 from tempfile import mkdtemp, NamedTemporaryFile
 from os.path import join, exists

mhctools/netchop.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2014-2017. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

mhctools/netmhc.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2015-2017. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 from subprocess import check_output
 import os
 

mhctools/netmhc3.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2015-2017. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

mhctools/netmhc4.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2015-2017. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 from .base_commandline_predictor import BaseCommandlinePredictor
 from .parsing import parse_netmhc4_stdout
 

mhctools/netmhc_cons.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2014-2017. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

mhctools/netmhc_pan.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2016-2017. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,7 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
 import logging
 from subprocess import check_output
 import os

mhctools/netmhc_pan28.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2014-2017. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

mhctools/netmhc_pan3.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2016-2017. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,7 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
 
 from .base_commandline_predictor import BaseCommandlinePredictor
 from .parsing import parse_netmhcpan3_stdout

mhctools/netmhc_pan4.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2016-2019. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

mhctools/netmhc_pan41.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2016-2023. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 from .base_commandline_predictor import BaseCommandlinePredictor
 from .parsing import parse_netmhc41_stdout
 from functools import partial

mhctools/netmhcii_pan.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2014-2017. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,8 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
-
 from functools import partial
 import logging
 import os

mhctools/parsing.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2014-2019. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at

mhctools/process_helpers.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2014. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -20,7 +18,7 @@
 from multiprocessing import cpu_count
 
 # pylint: disable=import-error
-from six.moves.queue import Queue
+from queue import Queue
 
 logger = logging.getLogger(__name__)
 

mhctools/random_predictor.py

@@ -1,5 +1,3 @@
-# Copyright (c) 2014-2017. Mount Sinai School of Medicine
-#
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
 # You may obtain a copy of the License at
@@ -12,7 +10,6 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
-from __future__ import print_function, division, absolute_import
 import random
 
 from .base_predictor import BasePredictor

requirements.txt

@@ -1,10 +1,8 @@
-numpy>=1.7
+numpy>=1.7,<2.0
 pandas>=0.13.1
-pyensembl>=1.0.3
+pyensembl>=1.0.3,
 varcode>=0.5.9
-six>=1.9.0
 pylint>=1.4.4
-nose>=1.3.6
-sercol>=0.0.2
+sercol>=0.0.2,<1.0.0
 mhcflurry>=2.0.0
 mhcnames>=0.3.2