From ae3d7e2fb9995c5c949a3a04d545d107bcfb5596 Mon Sep 17 00:00:00 2001
From: Tim O'Donnell <timodonnell@gmail.com>
Date: Tue, 19 Dec 2017 16:25:47 -0500
Subject: [PATCH] Better docstrings
---
mhcflurry/class1_affinity_predictor.py | 3 +++
mhcflurry/class1_neural_network.py | 27 ++++++++++++++++++++++++--
mhcflurry/common.py | 8 ++++++++
mhcflurry/downloads.py | 11 ++++++-----
4 files changed, 42 insertions(+), 7 deletions(-)
diff --git a/mhcflurry/class1_affinity_predictor.py b/mhcflurry/class1_affinity_predictor.py
index f1251282..7ba6a43b 100644
--- a/mhcflurry/class1_affinity_predictor.py
+++ b/mhcflurry/class1_affinity_predictor.py
@@ -153,6 +153,9 @@ class Class1AffinityPredictor(object):
@property
def num_networks(self):
+ """
+ Total number of neural networks (models)
+ """
return self.manifest_df.shape[0]
diff --git a/mhcflurry/class1_neural_network.py b/mhcflurry/class1_neural_network.py
index 07ee5a30..eafbbf96 100644
--- a/mhcflurry/class1_neural_network.py
+++ b/mhcflurry/class1_neural_network.py
@@ -48,15 +48,27 @@ class Class1NeuralNetwork(object):
}
],
)
+ """
+ Hyperparameters (and their default values) that affect the neural network
+ architecture.
+ """
compile_hyperparameter_defaults = HyperparameterDefaults(
loss="mse",
optimizer="rmsprop",
)
+ """
+ Loss and optimizer hyperparameters. Any values supported by keras may be
+ used.
+ """
input_encoding_hyperparameter_defaults = HyperparameterDefaults(
left_edge=4,
right_edge=4)
+ """
+ Number of amino acid residues that are given fixed positions on the each
+ side in the variable length encoding.
+ """
fit_hyperparameter_defaults = HyperparameterDefaults(
max_epochs=500,
@@ -70,6 +82,9 @@ class Class1NeuralNetwork(object):
random_negative_affinity_max=50000.0,
random_negative_match_distribution=True,
random_negative_distribution_smoothing=0.0)
+ """
+ Hyperparameters for neural network training.
+ """
early_stopping_hyperparameter_defaults = HyperparameterDefaults(
patience=10,
@@ -78,12 +93,18 @@ class Class1NeuralNetwork(object):
verbose=1, # currently unused
mode='auto' # currently unused
)
+ """
+ Hyperparameters for early stopping.
+ """
hyperparameter_defaults = network_hyperparameter_defaults.extend(
compile_hyperparameter_defaults).extend(
input_encoding_hyperparameter_defaults).extend(
fit_hyperparameter_defaults).extend(
early_stopping_hyperparameter_defaults)
+ """
+ Combined set of all supported hyperparameters and their default values.
+ """
def __init__(self, **hyperparameters):
self.hyperparameters = self.hyperparameter_defaults.with_defaults(
@@ -97,9 +118,11 @@ class Class1NeuralNetwork(object):
self.fit_seconds = None
self.fit_num_points = None
- # Process-wide keras model cache.
- # architecture JSON string -> (Keras model, existing network weights)
KERAS_MODELS_CACHE = {}
+ """
+ Process-wide keras model cache, a map from: architecture JSON string to
+ (Keras model, existing network weights)
+ """
@classmethod
def borrow_cached_network(klass, network_json, network_weights):
diff --git a/mhcflurry/common.py b/mhcflurry/common.py
index f87d235d..060dc4f6 100644
--- a/mhcflurry/common.py
+++ b/mhcflurry/common.py
@@ -71,6 +71,14 @@ def freeze_object(o):
def configure_logging(verbose=False):
+ """
+ Configure logging module using defaults.
+
+ Parameters
+ ----------
+ verbose : boolean
+ If true, output will be at level DEBUG, otherwise, INFO.
+ """
level = logging.DEBUG if verbose else logging.INFO
logging.basicConfig(
format="%(asctime)s.%(msecs)d %(levelname)s %(module)s - %(funcName)s:"
diff --git a/mhcflurry/downloads.py b/mhcflurry/downloads.py
index 81ef467e..21800feb 100644
--- a/mhcflurry/downloads.py
+++ b/mhcflurry/downloads.py
@@ -69,12 +69,13 @@ def get_current_release_downloads():
Return a dict of all available downloads in the current release.
The dict keys are the names of the downloads. The values are a dict
- with entries:
- downloaded : bool
- Whether the download is currently available locally
+ with two entries:
- metadata : dict
- Info about the download from downloads.yml such as URL
+ downloaded : bool
+ Whether the download is currently available locally
+
+ metadata : dict
+ Info about the download from downloads.yml such as URL
"""
downloads = (
get_downloads_metadata()
--
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