Refactor config parsing out. Use ruamel.yaml.

requirements.txt

@@ -3,4 +3,4 @@ scipy==0.19.0
 pandas==0.20.1
 matplotlib==2.0.1
 sklearn==0.0
-pyyaml==3.12
+ruamel.yaml==3.12

xlap/analyse/__init__.py

@@ -9,14 +9,6 @@ plt.rcParams.update({'figure.autolayout': True})
 
 # TODO: Refactor.
 
-def hist(df):
-    return df.hist(cumulative=True, normed=1, bins=200)
-
-
-def scatter(df, column):
-    plt.scatter(df.index, df[column], grid=True)
-
-
 def regress(df, column):
     x = df.index.values.reshape(-1, 1)
     y = df[column].values

xlap/analyse/jitter.py

@@ -29,11 +29,14 @@ def jitter_causes(df, durations, export=False, file_name=None):
     print("Outliers:", len(outliers), ";", "Threshold[us]:", threshold)
 
 
-def trace_jitter(df_filtered, export=False, file_name=None):
-    thresh = get_outlier_threshold(df_filtered["EndToEndTime"].describe())
-    df_no_outliers = df_filtered[df_filtered["EndToEndTime"] <= thresh]
+def trace_jitter(data_frame, export=False, file_name=None):
+    """
+    Displays (and saves) a stacked boxplot of durations.
+    """
+    thresh = get_outlier_threshold(data_frame["EndToEndTime"].describe())
+    df_no_outliers = data_frame[data_frame["EndToEndTime"] <= thresh]
     box(df_no_outliers, export, file_name)
-    print("{} / {} are no outliers.".format(len(df_no_outliers), len(df_filtered)))
+    print("{} / {} are no outliers.".format(len(df_no_outliers), len(data_frame)))
     fig = plt.gcf()
     fig.canvas.set_window_title('Jitter Analysis')
     plt.show()

xlap/analyse/util.py

+import matplotlib.pyplot as plt
+
+
+def hist(df):
+    return df.hist(cumulative=True, normed=1, bins=200)
+
+
+def scatter(df, column):
+    plt.scatter(df.index, df[column], grid=True)

xlap/command_line.py

 import argparse
-import yaml
 
-from xlap.parse import evaluate
+from xlap.parse import evaluate, parse_config
 import xlap.analyse.jitter as jitter
 
 tasks = {
@@ -9,12 +8,6 @@ tasks = {
 }
 
 
-def parse_config():
-    with open("xlap.yml") as f:
-        contents = f.read()
-    return yaml.load(contents)
-
-
 def main():
     config = parse_config()
     data_files = config["data_files"]

xlap/parse.py

 import pandas as pd
+import ruamel.yaml
+import ruamel.yaml as yaml
 
 
 def _stamp_name_by_src_and_type(all_stamps, src, kind=None):
@@ -77,3 +79,9 @@ def evaluate(sender_file, receiver_file, config, kind=0):
     df["EndToEndTime"] = df["Sender_D"] + df["Receiver_D"]
 
     return df
+
+
+def parse_config(file_name="xlap.yml"):
+    with open(file_name) as f:
+        contents = f.read()
+    return yaml.load(contents, Loader=ruamel.yaml.Loader)