switching from nose to pytest

tests/__init__.py

@@ -0,0 +1,11 @@
+# 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.

tests/test_binding_prediction.py

@@ -1,5 +1,17 @@
+# 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.
+
 from mhctools.binding_prediction import BindingPrediction
-from nose.tools import eq_
+from .common import eq_
 
 def test_binding_prediction_fields():
     bp = BindingPrediction(

tests/test_binding_prediction_collection.py

@@ -1,5 +1,17 @@
-from nose.tools import eq_
+# 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.
+
 from mhctools import BindingPrediction, BindingPredictionCollection
+from .common import eq_
 
 def test_collection_to_dataframe():
     bp = BindingPrediction(

tests/test_cli.py

@@ -1,8 +1,21 @@
-from mhctools.cli.script import parse_args, run_predictor
-from nose.tools import eq_
+# 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 tempfile
 from os import remove
 
+from mhctools.cli.script import parse_args, run_predictor
+from .common import eq_
+
 def test_peptides_without_subsequences():
     peptide = "SIINFEKLQY"
     args = parse_args([

tests/test_cli_parsing_helpers.py

@@ -1,5 +1,18 @@
-from nose.tools import eq_
+
+# 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.
+
 from mhctools.cli.parsing_helpers import parse_int_list
+from .common import eq_
 
 def test_parse_int_list():
     # int by itself

tests/test_iedb.py

@@ -1,6 +1,17 @@
-from nose.tools import assert_raises
+# 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.
 
 from mhctools import IedbNetMHCpan
+from .common import assert_raises
 
 
 DEFAULT_ALLELE = 'HLA-A*02:01'

tests/test_known_class1_epitopes.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

tests/test_known_class2_epitopes.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

tests/test_mhc_formats.py

@@ -1,3 +1,15 @@
+# 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.
+
 from mhctools.parsing import (
   parse_netmhcpan28_stdout,
   parse_netmhcpan3_stdout,

tests/test_mhcflurry.py

@@ -1,6 +1,18 @@
+# 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 sys
 
-from nose.tools import eq_, nottest
+from .common  import eq_
 from numpy import testing
 
 from mhcflurry import Class1AffinityPredictor
@@ -14,14 +26,6 @@
 }
 
 
-def skip_if_py2(function):
-    if sys.version_info[0] < 3:
-        print("MHCflurry requires python 3. Skipping test.")
-        return nottest(function)
-    return function
-
-
-@skip_if_py2
 def test_mhcflurry():
     predictor = MHCflurry(alleles=[DEFAULT_ALLELE])
     binding_predictions = predictor.predict_subsequences(

tests/test_mixmhcpred.py

@@ -1,7 +1,18 @@
+# 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.
+
 from tempfile import NamedTemporaryFile
-from os import remove
 from mhctools.mixmhcpred import parse_mixmhcpred_results
-from nose.tools import eq_
+from .common import eq_
 
 example_output =  """Peptide\tScore_bestAllele\tBestAllele\t%Rank_bestAllele\tScore_A0201\t%Rank_A0201
 MLDDFSAGA\t0.182093\tA0201\t0.3\t0.182093\t0.3

tests/test_netchop.py

@@ -1,3 +1,15 @@
+# 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.
+
 from numpy import testing
 
 from mhctools import NetChop

tests/test_netmhc_cons.py

@@ -1,3 +1,16 @@
+# 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.
+
+
 from mhctools import NetMHCcons
 from mhcnames import normalize_allele_name
 

tests/test_netmhc_pan.py

@@ -1,4 +1,16 @@
-from nose.tools import eq_
+# 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.
+
+from .common import eq_
 
 from mhctools import NetMHCpan
 

tests/test_netmhc_version.py

@@ -1,7 +1,7 @@
-from nose.tools import raises, eq_
 
 from mhctools import NetMHC, NetMHC3, NetMHC4
 from mhcnames import normalize_allele_name
+from .common import raises, eq_
 
 
 def run_class_with_executable(mhc_class, mhc_executable):

tests/test_netmhcii_pan.py

@@ -1,4 +1,16 @@
-from nose.tools import eq_
+# 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.
+
+from .common import eq_
 
 from mhctools import NetMHCIIpan
 from mhcnames import normalize_allele_name

tests/test_peptide_lengths.py

@@ -1,3 +1,15 @@
+# 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.
+
 
 """
 Class I predictors typically allow 8mer or longer peptides, whereas
@@ -6,7 +18,7 @@
 """
 
 from mhctools import NetMHCIIpan, NetMHC
-from nose.tools import eq_, assert_raises
+from .common import eq_, assert_raises
 
 
 def test_class2_9mer_success():

tests/test_random.py

@@ -1,6 +1,6 @@
 
-from nose.tools import eq_
 from mhctools import RandomBindingPredictor
+from .common import eq_
 
 
 alleles = [