From 4ea4173abd4625304048cb1fa9ae075d9566610e Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Sun, 10 Dec 2017 20:54:23 -0500
Subject: [PATCH] Refactor to simplify directory structure
---
.gitignore | 2 ++
mhcflurry/__init__.py | 6 ++---
.../class1_affinity_prediction/__init__.py | 9 -------
.../class1_affinity_predictor.py | 24 +++++++++----------
.../class1_neural_network.py | 8 +++----
mhcflurry/predict_command.py | 2 +-
.../train_allele_specific_models_command.py | 12 +++++-----
test/test_class1_neural_network.py | 2 +-
test/test_hyperparameters.py | 2 +-
...st_train_allele_specific_models_command.py | 11 ++++-----
10 files changed, 34 insertions(+), 44 deletions(-)
delete mode 100644 mhcflurry/class1_affinity_prediction/__init__.py
rename mhcflurry/{class1_affinity_prediction => }/class1_affinity_predictor.py (99%)
rename mhcflurry/{class1_affinity_prediction => }/class1_neural_network.py (98%)
rename mhcflurry/{class1_affinity_prediction => }/train_allele_specific_models_command.py (98%)
diff --git a/.gitignore b/.gitignore
index e44e3907..f09f2154 100644
--- a/.gitignore
+++ b/.gitignore
@@ -58,6 +58,8 @@ coverage.xml
# Sphinx documentation
docs/_build/
+docs/_static
+docs/_templates
# PyBuilder
target/
diff --git a/mhcflurry/__init__.py b/mhcflurry/__init__.py
index b909f853..e743fb33 100644
--- a/mhcflurry/__init__.py
+++ b/mhcflurry/__init__.py
@@ -12,10 +12,10 @@
# See the License for the specific language governing permissions and
# limitations under the License.
-from .class1_affinity_prediction.class1_neural_network import (
- Class1NeuralNetwork)
-from .class1_affinity_prediction.class1_affinity_predictor import (
+from mhcflurry.class1_affinity_predictor import (
Class1AffinityPredictor)
+from mhcflurry.class1_neural_network import (
+ Class1NeuralNetwork)
__version__ = "1.0.0"
diff --git a/mhcflurry/class1_affinity_prediction/__init__.py b/mhcflurry/class1_affinity_prediction/__init__.py
deleted file mode 100644
index 96707e88..00000000
--- a/mhcflurry/class1_affinity_prediction/__init__.py
+++ /dev/null
@@ -1,9 +0,0 @@
-from __future__ import absolute_import
-
-from .class1_neural_network import Class1NeuralNetwork
-from .class1_affinity_predictor import Class1AffinityPredictor
-
-__all__ = [
- 'Class1NeuralNetwork',
- 'Class1AffinityPredictor',
-]
diff --git a/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py b/mhcflurry/class1_affinity_predictor.py
similarity index 99%
rename from mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py
rename to mhcflurry/class1_affinity_predictor.py
index af94cfa0..f1251282 100644
--- a/mhcflurry/class1_affinity_prediction/class1_affinity_predictor.py
+++ b/mhcflurry/class1_affinity_predictor.py
@@ -1,26 +1,24 @@
import collections
-import time
import hashlib
import json
-from os.path import join, exists
-from six import string_types
import logging
-import warnings
import sys
+import time
+import warnings
+from os.path import join, exists
+import mhcnames
import numpy
import pandas
from numpy.testing import assert_equal
+from six import string_types
-import mhcnames
-
-from ..encodable_sequences import EncodableSequences
-from ..downloads import get_path
-from ..common import random_peptides
-from ..percent_rank_transform import PercentRankTransform
-from ..regression_target import to_ic50
-
-from .class1_neural_network import Class1NeuralNetwork
+from mhcflurry.class1_neural_network import Class1NeuralNetwork
+from mhcflurry.common import random_peptides
+from mhcflurry.downloads import get_path
+from mhcflurry.encodable_sequences import EncodableSequences
+from mhcflurry.percent_rank_transform import PercentRankTransform
+from mhcflurry.regression_target import to_ic50
class Class1AffinityPredictor(object):
diff --git a/mhcflurry/class1_affinity_prediction/class1_neural_network.py b/mhcflurry/class1_neural_network.py
similarity index 98%
rename from mhcflurry/class1_affinity_prediction/class1_neural_network.py
rename to mhcflurry/class1_neural_network.py
index a30d30b3..07ee5a30 100644
--- a/mhcflurry/class1_affinity_prediction/class1_neural_network.py
+++ b/mhcflurry/class1_neural_network.py
@@ -7,10 +7,10 @@ import pandas
from mhcflurry.hyperparameters import HyperparameterDefaults
-from ..encodable_sequences import EncodableSequences
-from ..amino_acid import available_vector_encodings, vector_encoding_length
-from ..regression_target import to_ic50, from_ic50
-from ..common import random_peptides, amino_acid_distribution
+from mhcflurry.encodable_sequences import EncodableSequences
+from mhcflurry.amino_acid import available_vector_encodings, vector_encoding_length
+from mhcflurry.regression_target import to_ic50, from_ic50
+from mhcflurry.common import random_peptides, amino_acid_distribution
class Class1NeuralNetwork(object):
diff --git a/mhcflurry/predict_command.py b/mhcflurry/predict_command.py
index f3a4a201..0b35d348 100644
--- a/mhcflurry/predict_command.py
+++ b/mhcflurry/predict_command.py
@@ -47,7 +47,7 @@ import logging
import pandas
from .downloads import get_path
-from .class1_affinity_prediction import Class1AffinityPredictor
+from .class1_affinity_predictor import Class1AffinityPredictor
parser = argparse.ArgumentParser(
diff --git a/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py b/mhcflurry/train_allele_specific_models_command.py
similarity index 98%
rename from mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py
rename to mhcflurry/train_allele_specific_models_command.py
index 46680fbf..8345ec9f 100644
--- a/mhcflurry/class1_affinity_prediction/train_allele_specific_models_command.py
+++ b/mhcflurry/train_allele_specific_models_command.py
@@ -2,21 +2,20 @@
Train Class1 single allele models.
"""
+import argparse
import os
+import signal
import sys
-import argparse
-import yaml
import time
-import signal
import traceback
from multiprocessing import Pool
import pandas
+import yaml
from mhcnames import normalize_allele_name
-from .class1_affinity_predictor import Class1AffinityPredictor
-from ..common import configure_logging
-
+from mhcflurry.class1_affinity_predictor import Class1AffinityPredictor
+from mhcflurry.common import configure_logging
parser = argparse.ArgumentParser(usage=__doc__)
@@ -89,6 +88,7 @@ parser.add_argument(
"Set to 1 for serial run. Set to 0 to use number of cores. "
"Default: %(default)s.")
+
def run(argv=sys.argv[1:]):
# On sigusr1 print stack trace
print("To show stack trace, run:\nkill -s USR1 %d" % os.getpid())
diff --git a/test/test_class1_neural_network.py b/test/test_class1_neural_network.py
index 8747f7e0..835c632d 100644
--- a/test/test_class1_neural_network.py
+++ b/test/test_class1_neural_network.py
@@ -2,7 +2,7 @@ import numpy
import pandas
numpy.random.seed(0)
-from mhcflurry import Class1NeuralNetwork
+from mhcflurry.class1_neural_network import Class1NeuralNetwork
from nose.tools import eq_
from numpy import testing
diff --git a/test/test_hyperparameters.py b/test/test_hyperparameters.py
index c1af6cac..0b887236 100644
--- a/test/test_hyperparameters.py
+++ b/test/test_hyperparameters.py
@@ -1,6 +1,6 @@
from numpy.testing import assert_equal
-from mhcflurry.class1_affinity_prediction import Class1NeuralNetwork
+from mhcflurry.class1_neural_network import Class1NeuralNetwork
def test_all_combinations_of_hyperparameters():
diff --git a/test/test_train_allele_specific_models_command.py b/test/test_train_allele_specific_models_command.py
index a556cc9a..affcde75 100644
--- a/test/test_train_allele_specific_models_command.py
+++ b/test/test_train_allele_specific_models_command.py
@@ -1,15 +1,14 @@
-import tempfile
-import shutil
-import os
import json
+import os
+import shutil
+import tempfile
from numpy.testing import assert_array_less, assert_equal
-from mhcflurry.class1_affinity_prediction import (
- train_allele_specific_models_command, Class1AffinityPredictor)
+from mhcflurry import train_allele_specific_models_command
+from mhcflurry import Class1AffinityPredictor
from mhcflurry.downloads import get_path
-
HYPERPARAMETERS = [
{
"n_models": 2,
--
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